Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001047.1 Hibiscus syriacus cultivar Beakdansim tig00002077_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 48882
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1903 original size:114 final size:113
Alignment explanation
Indices: 1698--2037 Score: 536
Period size: 114 Copynumber: 3.0 Consensus size: 113
1688 GATCATGTAG
* * * *
1698 TTCATCTTTCAATTCTAATGATTGGTTCTGTGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCTAATGATTGGTTTTG-GGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
1763 ACATTTCCAGAAGATGCTATTTGGTCTCCTTATTTCTACTATGAGCAAA
65 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* *
1812 TTCATCTTTCAAATCCAATGATTGGTTTTGGGATTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCTAATGATTGGTTTTGGG-TTCATACCAAACCAGATCAGATAACTCAAAGA
1877 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
65 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* * *
1926 TTCATCTTTTAAATCTAATGATTGGTTTTGGGGTTCATATCAAACCATATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCTAATGATTGGTTTT-GGGTTCATACCAAACCAGATCAGATAACTCAAAGA
**
1991 ACACTTCCAGAAGATGCTATTGGGTCTTATTATTTCTACTATGAGCA
65 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCA
2038 CATGGCACTT
Statistics
Matches: 209, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
113 2 0.01
114 204 0.98
115 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (113 bp):
TTCATCTTTCAAATCTAATGATTGGTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
CACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:4173 original size:7 final size:7
Alignment explanation
Indices: 4159--4221 Score: 55
Period size: 7 Copynumber: 9.4 Consensus size: 7
4149 TTTTTTTTCC
4159 TTTT-TT
1 TTTTCTT
4165 TTTTCTT
1 TTTTCTT
*
4172 TTTT-TGC
1 TTTTCT-T
4179 TTTTCTT
1 TTTTCTT
*
4186 TTTTATT
1 TTTTCTT
4193 TATTTCTT
1 T-TTTCTT
4201 TTTTC--
1 TTTTCTT
4206 -TTTCTT
1 TTTTCTT
4212 TTTTCTT
1 TTTTCTT
4219 TTT
1 TTT
4222 GTTGTTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
4 4 0.09
6 5 0.11
7 30 0.65
8 7 0.15
ACGTcount: A:0.03, C:0.11, G:0.02, T:0.84
Consensus pattern (7 bp):
TTTTCTT
Found at i:4211 original size:11 final size:11
Alignment explanation
Indices: 4151--4219 Score: 59
Period size: 11 Copynumber: 5.9 Consensus size: 11
4141 TTTCTCCCTT
*
4151 TTTTTTCCTTTT
1 TTTTTT-CTTTC
*
4163 TTTTTTCTTTTT
1 TTTTTTC-TTTC
4175 TTGCTTTTCTTT-
1 TT--TTTTCTTTC
*
4187 TTTATTTATTTC
1 TTT-TTTCTTTC
4199 TTTTTTCTTTC
1 TTTTTTCTTTC
4210 TTTTTTCTTT
1 TTTTTTCTTT
4220 TTGTTGTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
10 1 0.02
11 24 0.48
12 17 0.34
13 3 0.06
14 5 0.10
ACGTcount: A:0.03, C:0.13, G:0.01, T:0.83
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:7841 original size:8 final size:8
Alignment explanation
Indices: 7828--7852 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
7818 TACCAAATGC
7828 AAATGTAA
1 AAATGTAA
7836 AAATGTAA
1 AAATGTAA
7844 AAATGTAA
1 AAATGTAA
7852 A
1 A
7853 TGTAAATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (8 bp):
AAATGTAA
Found at i:9392 original size:18 final size:18
Alignment explanation
Indices: 9365--9410 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
9355 TAATACCTTC
*
9365 ATAA-ATAAAAAATATTA
1 ATAATATAAAAAATAATA
9382 ATAATAT-AAAAATAATA
1 ATAATATAAAAAATAATA
9399 AGTAATA-AAAAA
1 A-TAATATAAAAA
9411 TTTGAAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
ATAATATAAAAAATAATA
Found at i:9866 original size:26 final size:28
Alignment explanation
Indices: 9809--9866 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 28
9799 TATTTGATAT
9809 TAATAAATATTAACAATATAATAATTTA
1 TAATAAATATTAACAATATAATAATTTA
* **
9837 -AATAAA-ATTAA-ATTATAATTTTTTA
1 TAATAAATATTAACAATATAATAATTTA
9862 TAATA
1 TAATA
9867 TTTAATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 11 0.42
26 9 0.35
27 6 0.23
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (28 bp):
TAATAAATATTAACAATATAATAATTTA
Found at i:10061 original size:22 final size:20
Alignment explanation
Indices: 10019--10062 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
10009 ATGACTATAT
*
10019 AATAATAAAAAATAATATTA
1 AATAATAAAAAATAAAATTA
*
10039 AATATATAAACAAGTAAAATTA
1 AATA-ATAAA-AAATAAAATTA
10061 AA
1 AA
10063 ACATAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 5 0.25
22 11 0.55
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (20 bp):
AATAATAAAAAATAAAATTA
Found at i:11499 original size:12 final size:14
Alignment explanation
Indices: 11482--11554 Score: 69
Period size: 15 Copynumber: 5.1 Consensus size: 14
11472 ATTATTTTTT
*
11482 TAATAATAATATATA
1 TAATAATATTAT-TA
11497 TAATAATTATTATTA
1 TAATAA-TATTATTA
11512 TAATAATAATTATTA
1 TAATAAT-ATTATTA
* *
11527 T--TATTATTATAA
1 TAATAATATTATTA
11539 TAATAATAATTATTA
1 TAATAAT-ATTATTA
11554 T
1 T
11555 TATTATTATA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
12 7 0.15
13 3 0.06
14 4 0.08
15 29 0.60
16 5 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TAATAATATTATTA
Found at i:11500 original size:27 final size:27
Alignment explanation
Indices: 11470--11568 Score: 112
Period size: 27 Copynumber: 3.7 Consensus size: 27
11460 ATTGGGCCTG
* *
11470 TAATTATTTTTTTAATAATAATATATA
1 TAATTATTATTATAATAATAATATATA
* *
11497 TAATAATTATTATTATAATAATA-ATTA
1 TAATTATTATTATAATAATAATATA-TA
*
11524 TTATTATTATTATAATAATAATA-ATTA
1 TAATTATTATTATAATAATAATATA-TA
*
11551 TTATTATTATTATAATAA
1 TAATTATTATTATAATAA
11569 ATAAATAAGT
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
26 1 0.02
27 63 0.98
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TAATTATTATTATAATAATAATATATA
Found at i:11514 original size:24 final size:24
Alignment explanation
Indices: 11487--11568 Score: 112
Period size: 24 Copynumber: 3.4 Consensus size: 24
11477 TTTTTTAATA
11487 ATAAT-ATATATAATAATTATTATT
1 ATAATAATA-ATAATAATTATTATT
* *
11511 ATAATAATAATTATTATTATTATT
1 ATAATAATAATAATAATTATTATT
*
11535 ATAATAATAATAATTATTATTATT
1 ATAATAATAATAATAATTATTATT
*
11559 ATTATAATAA
1 ATAATAATAA
11569 ATAAATAAGT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
24 50 0.94
25 3 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
ATAATAATAATAATAATTATTATT
Found at i:11536 original size:30 final size:30
Alignment explanation
Indices: 11472--11563 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 30
11462 TGGGCCTGTA
* * * *
11472 ATTATTTTTTTAATAATAA-TATATATAATA
1 ATTATTATTATAATAATAATTAT-TATTATT
11502 ATTATTATTATAATAATAATTATTATTATT
1 ATTATTATTATAATAATAATTATTATTATT
11532 ATTA-TA--ATAATAATAATTATTATTATT
1 ATTATTATTATAATAATAATTATTATTATT
11559 ATTAT
1 ATTAT
11564 AATAAATAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
27 25 0.45
29 2 0.04
30 26 0.46
31 3 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
ATTATTATTATAATAATAATTATTATTATT
Found at i:11553 original size:3 final size:3
Alignment explanation
Indices: 11502--11563 Score: 61
Period size: 3 Copynumber: 20.7 Consensus size: 3
11492 ATATATAATA
* * * * * * *
11502 ATT ATT ATT ATA ATA ATA ATT ATT ATT ATT ATT ATA ATA ATA ATA ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
11550 ATT ATT ATT ATT AT
1 ATT ATT ATT ATT AT
11564 AATAAATAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (3 bp):
ATT
Found at i:13275 original size:24 final size:23
Alignment explanation
Indices: 13229--13280 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 23
13219 CTAAAACCTG
13229 TCTAATTTAAAAATATTTCTTTA
1 TCTAATTTAAAAATATTTCTTTA
13252 TTCTAA-TTAAAAATATAATT-TTTA
1 -TCTAATTTAAAAATAT--TTCTTTA
13276 TCTAA
1 TCTAA
13281 AACAGAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
23 15 0.58
24 9 0.35
25 2 0.08
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (23 bp):
TCTAATTTAAAAATATTTCTTTA
Found at i:13563 original size:2 final size:2
Alignment explanation
Indices: 13556--13581 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13546 CATTAAAATA
13556 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
13582 CCTTCTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13809 original size:38 final size:38
Alignment explanation
Indices: 13749--13836 Score: 135
Period size: 38 Copynumber: 2.4 Consensus size: 38
13739 AATAATCATA
13749 TCATA-TTC-TTTTTCATTCATATACATTTCAGAACTT
1 TCATATTTCATTTTTCATTCATATACATTTCAGAACTT
* * *
13785 TCATATTTTATTTTTCATTTATATATATTTCAGAACTT
1 TCATATTTCATTTTTCATTCATATACATTTCAGAACTT
13823 TCATATTTCATTTT
1 TCATATTTCATTTT
13837 CATCTTTCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 5 0.11
37 2 0.04
38 39 0.85
ACGTcount: A:0.27, C:0.15, G:0.02, T:0.56
Consensus pattern (38 bp):
TCATATTTCATTTTTCATTCATATACATTTCAGAACTT
Found at i:13828 original size:20 final size:20
Alignment explanation
Indices: 13764--13828 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
13754 TTCTTTTTCA
*
13764 TTCATATACATTTCAGAACT
1 TTCATATATATTTCAGAACT
* ***
13784 TTCATATTTTATTT-TTCA-T
1 TTCATA-TATATTTCAGAACT
13803 TT-ATATATATTTCAGAACT
1 TTCATATATATTTCAGAACT
13822 TTCATAT
1 TTCATAT
13829 TTCATTTTCA
Statistics
Matches: 32, Mismatches: 9, Indels: 8
0.65 0.18 0.16
Matches are distributed among these distances:
17 6 0.19
18 4 0.12
19 6 0.19
20 11 0.34
21 5 0.16
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.52
Consensus pattern (20 bp):
TTCATATATATTTCAGAACT
Found at i:13839 original size:13 final size:13
Alignment explanation
Indices: 13821--13888 Score: 70
Period size: 12 Copynumber: 5.4 Consensus size: 13
13811 ATTTCAGAAC
*
13821 TTTCATATTTCAT
1 TTTCACATTTCAT
*
13834 TTTCATC-TTTCAA
1 TTTCA-CATTTCAT
*
13847 TTTCACA-TTCAA
1 TTTCACATTTCAT
13859 TTTCACA-TTCAT
1 TTTCACATTTCAT
*
13871 TTTCACATCTCAT
1 TTTCACATTTCAT
13884 TTTCA
1 TTTCA
13889 TAACCAACAC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
12 24 0.50
13 24 0.50
ACGTcount: A:0.25, C:0.24, G:0.00, T:0.51
Consensus pattern (13 bp):
TTTCACATTTCAT
Found at i:14115 original size:27 final size:29
Alignment explanation
Indices: 14054--14115 Score: 67
Period size: 30 Copynumber: 2.2 Consensus size: 29
14044 GGCACTACAC
* *
14054 GGTGCTAATCATATCATAGGATGCACTCCAA
1 GGTGCAAATCATATCAT--GATGCACTCAAA
14085 -GTGCAAATCATATCAT-ATGCAC-CAAA
1 GGTGCAAATCATATCATGATGCACTCAAA
14111 GGTGC
1 GGTGC
14116 CATACATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
26 3 0.11
27 10 0.36
30 15 0.54
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (29 bp):
GGTGCAAATCATATCATGATGCACTCAAA
Found at i:17422 original size:4 final size:4
Alignment explanation
Indices: 17403--17460 Score: 57
Period size: 4 Copynumber: 14.2 Consensus size: 4
17393 TAAATCAAAG
* *
17403 ATAA A-AA A-AA ACTAA ATAA ATAA TTAA ATAA ATAA ATAA ATAG ATAA
1 ATAA ATAA ATAA A-TAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
17450 GATAA GATAA A
1 -ATAA -ATAA A
17461 GAAGAAAGGT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
3 6 0.13
4 29 0.62
5 12 0.26
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (4 bp):
ATAA
Found at i:19863 original size:105 final size:105
Alignment explanation
Indices: 19674--20345 Score: 1121
Period size: 105 Copynumber: 6.4 Consensus size: 105
19664 GTATTGTTCC
* *** * * *
19674 GAGTCCAATATCCTCCACCGTGGAGTTGAAATTGGTTCTGGAACTGG-GAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAATGGAGAAA-TGTTTGTTGACA
*
19738 ACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
19780 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATGGAGAAATGTTTGGTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATGGAGAAATGTTTGTTGACAAC
19845 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
19885 GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATGGAGAA-ATGTTTGTTGACAA
19950 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
19991 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATGGAGAAATGTTTGGTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATGGAGAAATGTTTGTTGACAAC
20056 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
20096 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGGAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATGGAGAAATGTTTGTTGACAAC
20161 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
20201 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATCGGCTCTGAAATTGAGAAATGTTTGTTGACAAT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATGGAGAAATGTTTGTTGACAAC
*
20266 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
20306 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
20346 GGTAAAACCT
Statistics
Matches: 535, Mismatches: 29, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
105 398 0.74
106 137 0.26
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.32
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATGGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:19915 original size:211 final size:211
Alignment explanation
Indices: 19674--20345 Score: 1150
Period size: 211 Copynumber: 3.2 Consensus size: 211
19664 GTATTGTTCC
* ** * * * *
19674 GAGTCCAATATCCTCCACCGTGGAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
19739 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
19804 GTTGAAATTGGCTCTGAAATGGAGAAATGTTTGGTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
131 GTTGAAATTGGCTCTGAAATGGAGAAATGTTTGGTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
19869 GAACTTGCGTTGTCTG
196 GAACTTGCGTTGTCTG
* * *
19885 GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
19950 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
20015 GTTGAAATTGGCTCTGAAATGGAGAAATGTTTGGTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
131 GTTGAAATTGGCTCTGAAATGGAGAAATGTTTGGTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
20080 GAACTTGCGTTGTCTG
196 GAACTTGCGTTGTCTG
* *
20096 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGG-AA-TGTTCGTTGACA
1 GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTG-GGAAATTGTTTGTTGACA
20159 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
* * * *
20224 AGTTGAAATCGGCTCTGAAATTGAGAAATGTTTGTTGACAATCAGCGGTCCCTTCGTCGTGAAGT
130 AGTTGAAATTGGCTCTGAAATGGAGAAATGTTTGGTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*
20289 TGAACTTGCGTTATCTG
195 TGAACTTGCGTTGTCTG
*
20306 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTG
20346 GGTAAAACCT
Statistics
Matches: 439, Mismatches: 21, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
210 192 0.44
211 246 0.56
212 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.32
Consensus pattern (211 bp):
GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
GTTGAAATTGGCTCTGAAATGGAGAAATGTTTGGTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
GAACTTGCGTTGTCTG
Found at i:21137 original size:52 final size:52
Alignment explanation
Indices: 21080--21179 Score: 139
Period size: 52 Copynumber: 1.9 Consensus size: 52
21070 TTCTTTTTTC
** *
21080 TCTTTTTTCTTTTTCAA-TTTAGGGTGCCCTTTCGGGTTTTCACCCTAAACGT
1 TCTTTTTTCTTTTTCAACTTT-GGACGCCCTCTCGGGTTTTCACCCTAAACGT
* *
21132 TCTTTTTTTTTTTTCAACTTTGGACGCCCTCTCGGGTTTTCATCCTAA
1 TCTTTTTTCTTTTTCAACTTTGGACGCCCTCTCGGGTTTTCACCCTAA
21180 GCGAAGTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
52 39 0.93
53 3 0.07
ACGTcount: A:0.13, C:0.24, G:0.14, T:0.49
Consensus pattern (52 bp):
TCTTTTTTCTTTTTCAACTTTGGACGCCCTCTCGGGTTTTCACCCTAAACGT
Found at i:30611 original size:20 final size:20
Alignment explanation
Indices: 30573--30616 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
30563 ATGGTTAGTA
*
30573 AAATAAAAATAAATGGAAAT
1 AAATAAAAATAAATAGAAAT
30593 AAATAAAAATAACA-AGAAAT
1 AAATAAAAATAA-ATAGAAAT
30613 AAAT
1 AAAT
30617 GGCAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (20 bp):
AAATAAAAATAAATAGAAAT
Found at i:31662 original size:4 final size:4
Alignment explanation
Indices: 31655--31700 Score: 56
Period size: 4 Copynumber: 11.0 Consensus size: 4
31645 TAAAAAAAAC
* *
31655 TAAA TAAA TAAT TAAA TAAA TAAA TAAA TAGA TAAGA TAAGA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA-A TAA-A TAAA
31701 GAAGAAAGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
4 28 0.76
5 9 0.24
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:32077 original size:11 final size:11
Alignment explanation
Indices: 32061--32092 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
32051 AATAAAGGGG
32061 AGGAAAGAAAA
1 AGGAAAGAAAA
32072 AGGAAAGAAAA
1 AGGAAAGAAAA
32083 AGGAAAGAAA
1 AGGAAAGAAA
32093 GAAAAATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (11 bp):
AGGAAAGAAAA
Found at i:34764 original size:20 final size:20
Alignment explanation
Indices: 34739--34778 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
34729 CGGTAAGCGG
34739 AAGATAAACATATTTAGCTT
1 AAGATAAACATATTTAGCTT
34759 AAGATAAACATATTTAGCTT
1 AAGATAAACATATTTAGCTT
34779 TGTCTGGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (20 bp):
AAGATAAACATATTTAGCTT
Done.